How to turn medical scans into models in Blender?
The overall goal is to extract some part from this scan and turn it into a simple and good looking mesh


It depends what is a good looking mesh according to you:
a mesh that that a same shape as the medical scan or a mesh with a good topology.

For a blender user, a good topology is very important is it will influence further modeling ( such as smooth of subsurf), UV mapping, Rendering time etc..


  •import and simplify the mesh in Blender


What do you mean by simplify? Change the topology in order to have fewer points? or make the mesh to only have quads?


  Other problems are harder to tackle because tissue or organs might not be easily separate-able 


In the CT scan, for each point, do you have some kind of additional information, such as tissue density, that would help to separete organs?


  Question: For these two problems, is there a preferred way about what should be done inside Blender and what not? Are there good tutorials about it?


One could see 2 options: 


Export the CT scan data in a format that can be import by blender.
Convert the CT data, in the some data point file (with a defined referential point, 3D coordinates, tissue density) like .csv and then use a python scrypt to import it into blender.